Formaldehyde Gel Electrophoresis of Total RNA

RNA has the tendency to form both secondary and tertiary structures that can impede its separation by electrophoresis. As such, identical species of RNA exhibiting varying degrees of intramolecular base pairing migrate at different rates and result in the smearing of distinct RNA molecules. Consequently, the electrophoresis of RNA needs to be performed under denaturing conditions. Heat denaturing the RNA sample prior to electrophoresis is insufficient, as secondary structures will simply reform unless a denaturing system is used.